X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=d5ddd1bbceb5f055ccc48157be84603ea09a4720;hb=048137e4ef1a2252d884afdd6ac8a12f0385eb16;hp=6d3f073abfd2d5341407a02e30f777b9cac19894;hpb=1a56a24b084eadd78387eabf71dc7114e356bd00;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 6d3f073..d5ddd1b 100755 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -81,6 +81,8 @@ public class PopupMenu extends JPopupMenu JMenuItem discoverPDB = new JMenuItem(); JMenu outputMenu = new JMenu(); JMenuItem sequenceFeature = new JMenuItem(); + JMenuItem textColour = new JMenuItem(); + JMenu jMenu1 = new JMenu(); /** * Creates a new PopupMenu object. @@ -178,7 +180,7 @@ public class PopupMenu extends JPopupMenu add(menuItem); if(ap.av.getSelectionGroup() !=null - && ap.av.getSelectionGroup().getSize(false)>1) + && ap.av.getSelectionGroup().getSize()>1) { menuItem = new JMenuItem("Represent Group with " + seq.getName()); menuItem.addActionListener(new java.awt.event.ActionListener() @@ -370,7 +372,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - groupName_actionPerformed(e); + groupName_actionPerformed(); } }); sequenceMenu.setText("Sequence"); @@ -379,7 +381,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - sequenceName_actionPerformed(e); + sequenceName_actionPerformed(); } }); PIDColour.setFocusPainted(false); @@ -388,7 +390,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - unGroupMenuItem_actionPerformed(e); + unGroupMenuItem_actionPerformed(); } }); @@ -397,7 +399,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - outline_actionPerformed(e); + outline_actionPerformed(); } }); nucleotideMenuItem.setText("Nucleotide"); @@ -405,7 +407,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - nucleotideMenuItem_actionPerformed(e); + nucleotideMenuItem_actionPerformed(); } }); colourMenu.setText("Group Colour"); @@ -415,7 +417,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - showBoxes_actionPerformed(e); + showBoxes_actionPerformed(); } }); showText.setText("Text"); @@ -424,7 +426,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - showText_actionPerformed(e); + showText_actionPerformed(); } }); showColourText.setText("Colour Text"); @@ -432,7 +434,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - showColourText_actionPerformed(e); + showColourText_actionPerformed(); } }); editMenu.setText("Edit"); @@ -441,7 +443,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - cut_actionPerformed(e); + cut_actionPerformed(); } }); upperCase.setText("To Upper Case"); @@ -457,7 +459,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - copy_actionPerformed(e); + copy_actionPerformed(); } }); lowerCase.setText("To Lower Case"); @@ -482,7 +484,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - pdbFromFile_actionPerformed(e); + pdbFromFile_actionPerformed(); } }); enterPDB.setText("Enter PDB Id"); @@ -490,7 +492,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - enterPDB_actionPerformed(e); + enterPDB_actionPerformed(); } }); discoverPDB.setText("Discover PDB ids"); @@ -498,7 +500,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - discoverPDB_actionPerformed(e); + discoverPDB_actionPerformed(); } }); outputMenu.setText("Output to Textbox..."); @@ -507,26 +509,28 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - sequenceFeature_actionPerformed(e); + sequenceFeature_actionPerformed(); } }); + textColour.setText("Text Colour"); + textColour.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + textColour_actionPerformed(); + } + }); + jMenu1.setText("Group"); add(groupMenu); add(sequenceMenu); groupMenu.add(editMenu); groupMenu.add(outputMenu); - groupMenu.addSeparator(); groupMenu.add(sequenceFeature); - groupMenu.addSeparator(); - groupMenu.add(groupName); - groupMenu.add(unGroupMenuItem); - groupMenu.add(colourMenu); - groupMenu.add(showBoxes); - groupMenu.add(showText); - groupMenu.add(showColourText); - groupMenu.add(outline); + groupMenu.add(jMenu1); sequenceMenu.add(sequenceName); sequenceMenu.add(pdbMenu); + colourMenu.add(textColour); colourMenu.add(noColourmenuItem); colourMenu.add(clustalColour); colourMenu.add(BLOSUM62Colour); @@ -573,12 +577,19 @@ public class PopupMenu extends JPopupMenu pdbMenu.add(pdbFromFile); pdbMenu.add(enterPDB); pdbMenu.add(discoverPDB); + jMenu1.add(groupName); + jMenu1.add(unGroupMenuItem); + jMenu1.add(colourMenu); + jMenu1.add(showBoxes); + jMenu1.add(showText); + jMenu1.add(showColourText); + jMenu1.add(outline); noColourmenuItem.setText("None"); noColourmenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - noColourmenuItem_actionPerformed(e); + noColourmenuItem_actionPerformed(); } }); @@ -587,7 +598,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - clustalColour_actionPerformed(e); + clustalColour_actionPerformed(); } }); zappoColour.setText("Zappo"); @@ -595,7 +606,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - zappoColour_actionPerformed(e); + zappoColour_actionPerformed(); } }); taylorColour.setText("Taylor"); @@ -603,7 +614,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - taylorColour_actionPerformed(e); + taylorColour_actionPerformed(); } }); hydrophobicityColour.setText("Hydrophobicity"); @@ -611,7 +622,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - hydrophobicityColour_actionPerformed(e); + hydrophobicityColour_actionPerformed(); } }); helixColour.setText("Helix propensity"); @@ -619,7 +630,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - helixColour_actionPerformed(e); + helixColour_actionPerformed(); } }); strandColour.setText("Strand propensity"); @@ -627,7 +638,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - strandColour_actionPerformed(e); + strandColour_actionPerformed(); } }); turnColour.setText("Turn propensity"); @@ -635,7 +646,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - turnColour_actionPerformed(e); + turnColour_actionPerformed(); } }); buriedColour.setText("Buried Index"); @@ -643,7 +654,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - buriedColour_actionPerformed(e); + buriedColour_actionPerformed(); } }); abovePIDColour.setText("Above % Identity"); @@ -651,7 +662,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - abovePIDColour_actionPerformed(e); + abovePIDColour_actionPerformed(); } }); userDefinedColour.setText("User Defined..."); @@ -667,7 +678,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - PIDColour_actionPerformed(e); + PIDColour_actionPerformed(); } }); BLOSUM62Colour.setText("BLOSUM62"); @@ -675,7 +686,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - BLOSUM62Colour_actionPerformed(e); + BLOSUM62Colour_actionPerformed(); } }); conservationMenuItem.setText("Conservation"); @@ -683,7 +694,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - conservationMenuItem_actionPerformed(e); + conservationMenuItem_actionPerformed(); } }); } @@ -704,10 +715,10 @@ public class PopupMenu extends JPopupMenu * * @param e DOCUMENT ME! */ - protected void clustalColour_actionPerformed(ActionEvent e) + protected void clustalColour_actionPerformed() { SequenceGroup sg = getGroup(); - sg.cs = new ClustalxColourScheme(sg.getSequences(true), + sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences), ap.av.alignment.getWidth()); refresh(); } @@ -717,7 +728,7 @@ public class PopupMenu extends JPopupMenu * * @param e DOCUMENT ME! */ - protected void zappoColour_actionPerformed(ActionEvent e) + protected void zappoColour_actionPerformed() { getGroup().cs = new ZappoColourScheme(); refresh(); @@ -728,7 +739,7 @@ public class PopupMenu extends JPopupMenu * * @param e DOCUMENT ME! */ - protected void taylorColour_actionPerformed(ActionEvent e) + protected void taylorColour_actionPerformed() { getGroup().cs = new TaylorColourScheme(); refresh(); @@ -739,7 +750,7 @@ public class PopupMenu extends JPopupMenu * * @param e DOCUMENT ME! */ - protected void hydrophobicityColour_actionPerformed(ActionEvent e) + protected void hydrophobicityColour_actionPerformed() { getGroup().cs = new HydrophobicColourScheme(); refresh(); @@ -750,7 +761,7 @@ public class PopupMenu extends JPopupMenu * * @param e DOCUMENT ME! */ - protected void helixColour_actionPerformed(ActionEvent e) + protected void helixColour_actionPerformed() { getGroup().cs = new HelixColourScheme(); refresh(); @@ -761,7 +772,7 @@ public class PopupMenu extends JPopupMenu * * @param e DOCUMENT ME! */ - protected void strandColour_actionPerformed(ActionEvent e) + protected void strandColour_actionPerformed() { getGroup().cs = new StrandColourScheme(); refresh(); @@ -772,7 +783,7 @@ public class PopupMenu extends JPopupMenu * * @param e DOCUMENT ME! */ - protected void turnColour_actionPerformed(ActionEvent e) + protected void turnColour_actionPerformed() { getGroup().cs = new TurnColourScheme(); refresh(); @@ -783,7 +794,7 @@ public class PopupMenu extends JPopupMenu * * @param e DOCUMENT ME! */ - protected void buriedColour_actionPerformed(ActionEvent e) + protected void buriedColour_actionPerformed() { getGroup().cs = new BuriedColourScheme(); refresh(); @@ -794,7 +805,7 @@ public class PopupMenu extends JPopupMenu * * @param e DOCUMENT ME! */ - public void nucleotideMenuItem_actionPerformed(ActionEvent e) + public void nucleotideMenuItem_actionPerformed() { getGroup().cs = new NucleotideColourScheme(); refresh(); @@ -805,7 +816,7 @@ public class PopupMenu extends JPopupMenu * * @param e DOCUMENT ME! */ - protected void abovePIDColour_actionPerformed(ActionEvent e) + protected void abovePIDColour_actionPerformed() { SequenceGroup sg = getGroup(); if(sg.cs==null) @@ -814,7 +825,7 @@ public class PopupMenu extends JPopupMenu if (abovePIDColour.isSelected()) { sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(true), sg.getStartRes(), + sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg.getEndRes() + 1)); int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, @@ -857,11 +868,11 @@ public class PopupMenu extends JPopupMenu * * @param e DOCUMENT ME! */ - protected void PIDColour_actionPerformed(ActionEvent e) + protected void PIDColour_actionPerformed() { SequenceGroup sg = getGroup(); sg.cs = new PIDColourScheme(); - sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), + sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg.getEndRes() + 1)); refresh(); @@ -872,13 +883,13 @@ public class PopupMenu extends JPopupMenu * * @param e DOCUMENT ME! */ - protected void BLOSUM62Colour_actionPerformed(ActionEvent e) + protected void BLOSUM62Colour_actionPerformed() { SequenceGroup sg = getGroup(); sg.cs = new Blosum62ColourScheme(); - sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), + sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg.getEndRes() + 1)); @@ -890,7 +901,7 @@ public class PopupMenu extends JPopupMenu * * @param e DOCUMENT ME! */ - protected void noColourmenuItem_actionPerformed(ActionEvent e) + protected void noColourmenuItem_actionPerformed() { getGroup().cs = null; refresh(); @@ -901,7 +912,7 @@ public class PopupMenu extends JPopupMenu * * @param e DOCUMENT ME! */ - protected void conservationMenuItem_actionPerformed(ActionEvent e) + protected void conservationMenuItem_actionPerformed() { SequenceGroup sg = getGroup(); if(sg.cs==null) @@ -911,7 +922,7 @@ public class PopupMenu extends JPopupMenu { Conservation c = new Conservation("Group", ResidueProperties.propHash, 3, - sg.getSequences(true), + sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg.getEndRes() + 1); @@ -936,48 +947,26 @@ public class PopupMenu extends JPopupMenu * * @param e DOCUMENT ME! */ - protected void groupName_actionPerformed(ActionEvent e) + protected void groupName_actionPerformed() { - SequenceGroup sg = getGroup(); - String reply = JOptionPane.showInternalInputDialog(Desktop.desktop, - "Enter new group name", "Edit group name", - JOptionPane.QUESTION_MESSAGE); - if (reply == null) - { - return; - } + SequenceGroup sg = getGroup(); + EditNameDialog dialog = new EditNameDialog(sg.getName(), + sg.getDescription(), + " Group Name ", + "Group Description ", + "Edit Group Name/Description"); - sg.setName(reply); - groupName.setText(reply); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void analyze_actionPerformed(ActionEvent e) - { - CutAndPasteTransfer cap = new CutAndPasteTransfer(); - JInternalFrame frame = new JInternalFrame(); - frame.setContentPane(cap); - Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300); - - SequenceGroup sg = getGroup(); - StringBuffer sb = new StringBuffer(); - - for (int i = 0; i < sg.getSize(false); i++) - { - Sequence tmp = (Sequence) sg.getSequences(false).elementAt(i); - sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1)); - sb.append("\n"); - } + if (!dialog.accept) + { + return; + } - sb.append("Something amazing will happen soon"); - cap.setText(sb.toString()); + sg.setName(dialog.getName()); + sg.setDescription(dialog.getDescription()); } + /** * DOCUMENT ME! * @@ -998,40 +987,22 @@ public class PopupMenu extends JPopupMenu * * @param e DOCUMENT ME! */ - void sequenceName_actionPerformed(ActionEvent e) + void sequenceName_actionPerformed() { - JLabel idlabel = new JLabel( " Sequence Name "); - JLabel desclabel = new JLabel("Sequence Description "); - idlabel.setFont(new Font("Courier", Font.PLAIN, 12)); - desclabel.setFont(new Font("Courier", Font.PLAIN, 12)); - JTextField id = new JTextField(sequence.getName(), 40); - JTextField description = new JTextField(sequence.getDescription(), 40); - JPanel panel = new JPanel(new BorderLayout()); - JPanel panel2 = new JPanel(new BorderLayout()); - panel2.add(idlabel, BorderLayout.WEST); - panel2.add(id, BorderLayout.CENTER); - panel.add(panel2, BorderLayout.NORTH); - panel2 = new JPanel(new BorderLayout()); - panel2.add(desclabel, BorderLayout.WEST); - panel2.add(description, BorderLayout.CENTER); - panel.add(panel2, BorderLayout.SOUTH); - - - int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop, - panel, "Edit Sequence Name/Description", - JOptionPane.OK_CANCEL_OPTION ); - - - if (reply != JOptionPane.OK_OPTION ) + EditNameDialog dialog = new EditNameDialog(sequence.getName(), + sequence.getDescription(), + " Sequence Name ", + "Sequence Description ", + "Edit Sequence Name/Description"); + + if (!dialog.accept) { return; } - String s = id.getText(); - - if (s != null) + if (dialog.getName() != null) { - if (s.indexOf(" ") > -1) + if (dialog.getName().indexOf(" ") > -1) { JOptionPane.showMessageDialog(ap, "Spaces have been converted to \"_\"", @@ -1039,12 +1010,11 @@ public class PopupMenu extends JPopupMenu JOptionPane.WARNING_MESSAGE); } - s = s.replace(' ', '_'); - sequence.setName(s); + sequence.setName(dialog.getName().replace(' ', '_')); ap.repaint(); } - sequence.setDescription(description.getText()); + sequence.setDescription(dialog.getDescription()); ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences()); @@ -1056,7 +1026,7 @@ public class PopupMenu extends JPopupMenu * * @param e DOCUMENT ME! */ - void unGroupMenuItem_actionPerformed(ActionEvent e) + void unGroupMenuItem_actionPerformed() { SequenceGroup sg = ap.av.getSelectionGroup(); ap.av.alignment.deleteGroup(sg); @@ -1070,7 +1040,7 @@ public class PopupMenu extends JPopupMenu * * @param e DOCUMENT ME! */ - protected void outline_actionPerformed(ActionEvent e) + protected void outline_actionPerformed() { SequenceGroup sg = getGroup(); Color col = JColorChooser.showDialog(this, "Select Outline Colour", @@ -1089,7 +1059,7 @@ public class PopupMenu extends JPopupMenu * * @param e DOCUMENT ME! */ - public void showBoxes_actionPerformed(ActionEvent e) + public void showBoxes_actionPerformed() { getGroup().setDisplayBoxes(showBoxes.isSelected()); refresh(); @@ -1100,7 +1070,7 @@ public class PopupMenu extends JPopupMenu * * @param e DOCUMENT ME! */ - public void showText_actionPerformed(ActionEvent e) + public void showText_actionPerformed() { getGroup().setDisplayText(showText.isSelected()); refresh(); @@ -1111,7 +1081,7 @@ public class PopupMenu extends JPopupMenu * * @param e DOCUMENT ME! */ - public void showColourText_actionPerformed(ActionEvent e) + public void showColourText_actionPerformed() { getGroup().setColourText(showColourText.isSelected()); refresh(); @@ -1138,42 +1108,41 @@ public class PopupMenu extends JPopupMenu void hideSequences(boolean representGroup) { SequenceGroup sg = ap.av.getSelectionGroup(); - if(sg==null || sg.getSize(false)<1) + if(sg==null || sg.getSize()<1) { ap.av.hideSequence(new SequenceI[]{sequence}); return; } - int gsize = sg.getSize(false); - SequenceI [] hseqs; + ap.av.setSelectionGroup(null); - hseqs = new SequenceI[ representGroup ? gsize-1 : gsize ]; + if (representGroup) + { + ap.av.hideRepSequences(sequence, sg); - int index = 0; - for(int i=0; i